Starting phenix.real_space_refine
on Wed Mar 12 01:47:18 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8toh_41452/03_2025/8toh_41452.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8toh_41452/03_2025/8toh_41452.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.29
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8toh_41452/03_2025/8toh_41452.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8toh_41452/03_2025/8toh_41452.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8toh_41452/03_2025/8toh_41452.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8toh_41452/03_2025/8toh_41452.cif"
  }
  resolution = 3.29
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.032
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      25      5.16       5
     C    4554      2.51       5
     N    1199      2.21       5
     O    1244      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7022
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7022
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 860, 7022
          Classifications: {'peptide': 860}
          Link IDs: {'PTRANS': 49, 'TRANS': 810}
          Chain breaks: 2
  Time building chain proxies: 4.51, per 1000 atoms: 0.64
  Number of scatterers: 7022
  At special positions: 0
  Unit cell: (72.8784, 76.1319, 115.825, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      25     16.00
     O    1244      8.00
     N    1199      7.00
     C    4554      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.52
  Conformation dependent library (CDL) restraints added in 901.2 milliseconds
  

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1600

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 8 sheets defined
      47.1% alpha, 9.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 36 through 38
      No H-bonds generated for 'chain 'A' and resid 36 through 38'
    Processing helix  chain 'A' and resid 39 through 45
      removed outlier: 4.317A  pdb=" N   ALA A  43 " --> pdb=" O   ALA A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 56
    Processing helix  chain 'A' and resid 72 through 77
      removed outlier: 3.598A  pdb=" N   THR A  76 " --> pdb=" O   ALA A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 85
    Processing helix  chain 'A' and resid 88 through 96
      removed outlier: 3.866A  pdb=" N   THR A  92 " --> pdb=" O   SER A  88 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   HIS A  95 " --> pdb=" O   ASP A  91 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   HIS A  96 " --> pdb=" O   THR A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 125
      removed outlier: 3.774A  pdb=" N   VAL A 124 " --> pdb=" O   THR A 121 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   ALA A 125 " --> pdb=" O   GLY A 122 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 121 through 125'
    Processing helix  chain 'A' and resid 132 through 143
      removed outlier: 3.750A  pdb=" N   THR A 136 " --> pdb=" O   VAL A 132 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ALA A 138 " --> pdb=" O   ARG A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 184
    Processing helix  chain 'A' and resid 198 through 203
      removed outlier: 4.187A  pdb=" N   ALA A 203 " --> pdb=" O   ARG A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 209
      removed outlier: 4.245A  pdb=" N   ALA A 208 " --> pdb=" O   GLY A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 228
      removed outlier: 4.011A  pdb=" N   ASP A 214 " --> pdb=" O   ARG A 210 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ARG A 217 " --> pdb=" O   ALA A 213 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   TYR A 219 " --> pdb=" O   HIS A 215 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ALA A 220 " --> pdb=" O   PHE A 216 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU A 222 " --> pdb=" O   ASP A 218 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   PHE A 224 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   ARG A 225 " --> pdb=" O   GLU A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 239 through 249
      removed outlier: 3.541A  pdb=" N   HIS A 246 " --> pdb=" O   VAL A 242 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLY A 247 " --> pdb=" O   VAL A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 286
      removed outlier: 3.962A  pdb=" N   GLY A 264 " --> pdb=" O   SER A 260 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LEU A 266 " --> pdb=" O   ARG A 262 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   LEU A 281 " --> pdb=" O   LYS A 277 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   THR A 284 " --> pdb=" O   HIS A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 290
    Processing helix  chain 'A' and resid 309 through 324
      removed outlier: 3.552A  pdb=" N   VAL A 323 " --> pdb=" O   SER A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 333
      Proline residue:  A 330  - end of helix
      removed outlier: 3.639A  pdb=" N   ILE A 333 " --> pdb=" O   LYS A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 345
      removed outlier: 3.502A  pdb=" N   LYS A 342 " --> pdb=" O   PRO A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 361
      removed outlier: 3.666A  pdb=" N   LYS A 358 " --> pdb=" O   GLU A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 386
      removed outlier: 3.558A  pdb=" N   PHE A 386 " --> pdb=" O   HIS A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 405
      removed outlier: 3.578A  pdb=" N   SER A 399 " --> pdb=" O   ARG A 395 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   TRP A 400 " --> pdb=" O   GLN A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 448
      removed outlier: 3.918A  pdb=" N   TYR A 432 " --> pdb=" O   ALA A 428 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LEU A 442 " --> pdb=" O   ILE A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 470
      No H-bonds generated for 'chain 'A' and resid 468 through 470'
    Processing helix  chain 'A' and resid 491 through 502
      removed outlier: 3.879A  pdb=" N   ILE A 501 " --> pdb=" O   TYR A 497 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   GLU A 502 " --> pdb=" O   GLN A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 589
      removed outlier: 4.360A  pdb=" N   GLN A 581 " --> pdb=" O   ALA A 577 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLU A 587 " --> pdb=" O   ALA A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 603
    Processing helix  chain 'A' and resid 612 through 629
      removed outlier: 3.844A  pdb=" N   LEU A 616 " --> pdb=" O   ASN A 612 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   TYR A 619 " --> pdb=" O   ILE A 615 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ARG A 620 " --> pdb=" O   LEU A 616 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 661 through 678
      removed outlier: 3.584A  pdb=" N   TYR A 669 " --> pdb=" O   ALA A 665 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   GLU A 676 " --> pdb=" O   LEU A 672 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 696 through 718
      removed outlier: 3.964A  pdb=" N   ASN A 702 " --> pdb=" O   SER A 698 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ALA A 708 " --> pdb=" O   LEU A 704 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 742 through 757
      removed outlier: 3.721A  pdb=" N   LYS A 746 " --> pdb=" O   SER A 742 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   GLU A 750 " --> pdb=" O   LYS A 746 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ARG A 751 " --> pdb=" O   GLU A 747 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 771 through 781
    Processing helix  chain 'A' and resid 790 through 798
      removed outlier: 3.759A  pdb=" N   LYS A 795 " --> pdb=" O   GLU A 791 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   LEU A 796 " --> pdb=" O   ASP A 792 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ILE A 797 " --> pdb=" O   GLU A 793 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   GLN A 798 " --> pdb=" O   LYS A 794 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 850 through 864
      removed outlier: 3.555A  pdb=" N   LYS A 854 " --> pdb=" O   TRP A 850 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   VAL A 855 " --> pdb=" O   GLY A 851 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   LYS A 860 " --> pdb=" O   LEU A 856 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 884 through 904
      removed outlier: 3.699A  pdb=" N   TYR A 889 " --> pdb=" O   GLN A 885 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   GLN A 892 " --> pdb=" O   VAL A 888 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ALA A 901 " --> pdb=" O   GLU A 897 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   HIS A 902 " --> pdb=" O   ALA A 898 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 939 through 951
      removed outlier: 3.652A  pdb=" N   HIS A 943 " --> pdb=" O   ALA A 939 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ILE A 947 " --> pdb=" O   HIS A 943 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 69
      removed outlier: 7.840A  pdb=" N   ILE A 410 " --> pdb=" O   ILE A 453 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   TYR A 455 " --> pdb=" O   ILE A 410 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   ILE A 412 " --> pdb=" O   TYR A 455 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   ALA A 457 " --> pdb=" O   ILE A 412 " (cutoff:3.500A)
      removed outlier: 7.156A  pdb=" N   GLU A 414 " --> pdb=" O   ALA A 457 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU A 369 " --> pdb=" O   PHE A 411 " (cutoff:3.500A)
      removed outlier: 5.442A  pdb=" N   PHE A 366 " --> pdb=" O   VAL A 294 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   ILE A 296 " --> pdb=" O   PHE A 366 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   TRP A 234 " --> pdb=" O   SER A 295 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   ALA A 297 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
      removed outlier: 7.183A  pdb=" N   THR A 236 " --> pdb=" O   ALA A 297 " (cutoff:3.500A)
      removed outlier: 12.037A  pdb=" N   SER A 299 " --> pdb=" O   THR A 236 " (cutoff:3.500A)
      removed outlier: 10.423A  pdb=" N   ASP A 238 " --> pdb=" O   SER A 299 " (cutoff:3.500A)
      removed outlier: 8.080A  pdb=" N   ILE A 235 " --> pdb=" O   PRO A 187 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   VAL A 189 " --> pdb=" O   ILE A 235 " (cutoff:3.500A)
      removed outlier: 7.714A  pdb=" N   ILE A 237 " --> pdb=" O   VAL A 189 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   TYR A 147 " --> pdb=" O   VAL A 188 " (cutoff:3.500A)
      removed outlier: 7.727A  pdb=" N   THR A 190 " --> pdb=" O   TYR A 147 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   PHE A 149 " --> pdb=" O   THR A 190 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 302 through 304
      removed outlier: 4.048A  pdb=" N   TRP A 302 " --> pdb=" O   SER A 391 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   SER A 391 " --> pdb=" O   TRP A 302 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   LEU A 389 " --> pdb=" O   ASN A 304 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 419 through 420
    Processing sheet with id=AA4, first strand: chain 'A' and resid 594 through 595
      removed outlier: 5.807A  pdb=" N   VAL A 527 " --> pdb=" O   ARG A 594 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 634 through 635
      removed outlier: 5.701A  pdb=" N   VAL A 635 " --> pdb=" O   ILE A 685 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   MET A 687 " --> pdb=" O   VAL A 635 " (cutoff:3.500A)
      removed outlier: 6.127A  pdb=" N   TRP A 684 " --> pdb=" O   SER A 727 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   ALA A 729 " --> pdb=" O   TRP A 684 " (cutoff:3.500A)
      removed outlier: 7.037A  pdb=" N   THR A 686 " --> pdb=" O   ALA A 729 " (cutoff:3.500A)
      removed outlier: 11.642A  pdb=" N   GLN A 731 " --> pdb=" O   THR A 686 " (cutoff:3.500A)
      removed outlier: 11.204A  pdb=" N   ASN A 688 " --> pdb=" O   GLN A 731 " (cutoff:3.500A)
      removed outlier: 9.200A  pdb=" N   ALA A 805 " --> pdb=" O   ILE A 726 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   ILE A 728 " --> pdb=" O   ALA A 805 " (cutoff:3.500A)
      removed outlier: 7.783A  pdb=" N   SER A 807 " --> pdb=" O   ILE A 728 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   LEU A 730 " --> pdb=" O   SER A 807 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   LEU A 804 " --> pdb=" O   TYR A 869 " (cutoff:3.500A)
      removed outlier: 6.094A  pdb=" N   ILE A 871 " --> pdb=" O   LEU A 804 " (cutoff:3.500A)
      removed outlier: 7.424A  pdb=" N   LEU A 806 " --> pdb=" O   ILE A 871 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 734 through 737
      removed outlier: 3.503A  pdb=" N   GLU A 736 " --> pdb=" O   ILE A 812 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   VAL A 814 " --> pdb=" O   GLU A 736 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 824 through 825
    Processing sheet with id=AA8, first strand: chain 'A' and resid 928 through 931
      removed outlier: 3.605A  pdb=" N   ARG A 929 " --> pdb=" O   GLU A 936 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLU A 936 " --> pdb=" O   ARG A 929 " (cutoff:3.500A)

    228 hydrogen bonds defined for protein.
    657 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.01

  Time building geometry restraints manager: 1.84 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.23 -     1.34: 2248
        1.34 -     1.46: 1791
        1.46 -     1.58: 3168
        1.58 -     1.69: 0
        1.69 -     1.81: 42
  Bond restraints: 7249
  Sorted by residual:
  bond pdb=" C   TRP A 638 "
       pdb=" N   GLN A 639 "
    ideal  model  delta    sigma   weight residual
    1.329  1.358 -0.029 1.35e-02 5.49e+03 4.65e+00
  bond pdb=" CB  PRO A  35 "
       pdb=" CG  PRO A  35 "
    ideal  model  delta    sigma   weight residual
    1.492  1.573 -0.081 5.00e-02 4.00e+02 2.62e+00
  bond pdb=" C   ALA A 254 "
       pdb=" N   PRO A 255 "
    ideal  model  delta    sigma   weight residual
    1.328  1.346 -0.018 1.25e-02 6.40e+03 2.10e+00
  bond pdb=" CB  LYS A 329 "
       pdb=" CG  LYS A 329 "
    ideal  model  delta    sigma   weight residual
    1.520  1.555 -0.035 3.00e-02 1.11e+03 1.34e+00
  bond pdb=" CB  GLN A 230 "
       pdb=" CG  GLN A 230 "
    ideal  model  delta    sigma   weight residual
    1.520  1.553 -0.033 3.00e-02 1.11e+03 1.22e+00
  ... (remaining 7244 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 9572
        1.52 -     3.04: 253
        3.04 -     4.57: 24
        4.57 -     6.09: 8
        6.09 -     7.61: 5
  Bond angle restraints: 9862
  Sorted by residual:
  angle pdb=" N   VAL A 132 "
        pdb=" CA  VAL A 132 "
        pdb=" C   VAL A 132 "
      ideal   model   delta    sigma   weight residual
     113.47  109.22    4.25 1.01e+00 9.80e-01 1.77e+01
  angle pdb=" CB  LYS A 329 "
        pdb=" CG  LYS A 329 "
        pdb=" CD  LYS A 329 "
      ideal   model   delta    sigma   weight residual
     111.30  118.91   -7.61 2.30e+00 1.89e-01 1.10e+01
  angle pdb=" CA  LYS A 329 "
        pdb=" CB  LYS A 329 "
        pdb=" CG  LYS A 329 "
      ideal   model   delta    sigma   weight residual
     114.10  120.54   -6.44 2.00e+00 2.50e-01 1.04e+01
  angle pdb=" CA  GLN A 230 "
        pdb=" CB  GLN A 230 "
        pdb=" CG  GLN A 230 "
      ideal   model   delta    sigma   weight residual
     114.10  119.61   -5.51 2.00e+00 2.50e-01 7.60e+00
  angle pdb=" CA  GLN A 731 "
        pdb=" CB  GLN A 731 "
        pdb=" CG  GLN A 731 "
      ideal   model   delta    sigma   weight residual
     114.10  119.58   -5.48 2.00e+00 2.50e-01 7.50e+00
  ... (remaining 9857 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.19: 3649
       15.19 -    30.37: 402
       30.37 -    45.55: 115
       45.55 -    60.74: 23
       60.74 -    75.92: 7
  Dihedral angle restraints: 4196
    sinusoidal: 1695
      harmonic: 2501
  Sorted by residual:
  dihedral pdb=" CA  HIS A 880 "
           pdb=" C   HIS A 880 "
           pdb=" N   ALA A 881 "
           pdb=" CA  ALA A 881 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.30   20.70     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" CA  THR A 632 "
           pdb=" C   THR A 632 "
           pdb=" N   PRO A 633 "
           pdb=" CA  PRO A 633 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.49  -18.51     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CA  ILE A 438 "
           pdb=" C   ILE A 438 "
           pdb=" N   MET A 439 "
           pdb=" CA  MET A 439 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.31   17.69     0      5.00e+00 4.00e-02 1.25e+01
  ... (remaining 4193 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 590
       0.029 -    0.057: 267
       0.057 -    0.086: 97
       0.086 -    0.115: 48
       0.115 -    0.143: 9
  Chirality restraints: 1011
  Sorted by residual:
  chirality pdb=" CA  ILE A 870 "
            pdb=" N   ILE A 870 "
            pdb=" C   ILE A 870 "
            pdb=" CB  ILE A 870 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.12e-01
  chirality pdb=" CA  ILE A 685 "
            pdb=" N   ILE A 685 "
            pdb=" C   ILE A 685 "
            pdb=" CB  ILE A 685 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.48e-01
  chirality pdb=" CA  TRP A 279 "
            pdb=" N   TRP A 279 "
            pdb=" C   TRP A 279 "
            pdb=" CB  TRP A 279 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.34e-01
  ... (remaining 1008 not shown)

  Planarity restraints: 1273
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 279 "   -0.031 2.00e-02 2.50e+03   2.30e-02 1.32e+01
        pdb=" CG  TRP A 279 "    0.061 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 279 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 279 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 279 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 279 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 279 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 279 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 279 "   -0.009 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 279 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 689 "    0.039 5.00e-02 4.00e+02   5.93e-02 5.63e+00
        pdb=" N   PRO A 690 "   -0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO A 690 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 690 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 260 "   -0.026 5.00e-02 4.00e+02   3.97e-02 2.53e+00
        pdb=" N   PRO A 261 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A 261 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 261 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1270 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1209
        2.76 -     3.30: 7073
        3.30 -     3.83: 12180
        3.83 -     4.37: 14197
        4.37 -     4.90: 23515
  Nonbonded interactions: 58174
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 873 "
            pdb=" OH  TYR A 912 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" O   SER A 596 "
            pdb=" OH  TYR A 619 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" NH2 ARG A 148 "
            pdb=" OD2 ASP A 238 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" NH2 ARG A 134 "
            pdb=" O   ASP A 485 "
     model   vdw
     2.244 3.120
  nonbonded pdb=" OG1 THR A  92 "
            pdb=" NE2 GLN A 198 "
     model   vdw
     2.255 3.120
  ... (remaining 58169 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     18.990
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6433
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.081   7249  Z= 0.160
  Angle     :  0.582   7.611   9862  Z= 0.317
  Chirality :  0.041   0.143   1011
  Planarity :  0.004   0.059   1273
  Dihedral  : 14.462  75.924   2596
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 13.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.28), residues: 854
  helix: -0.54 (0.29), residues: 316
  sheet: -0.66 (0.59), residues: 85
  loop : -1.61 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.061   0.002   TRP A 279 
 HIS   0.006   0.001   HIS A 146 
 PHE   0.016   0.001   PHE A 332 
 TYR   0.011   0.001   TYR A 531 
 ARG   0.003   0.000   ARG A 671 

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.685 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 GLN cc_start: 0.6649 (tm-30) cc_final: 0.6379 (pt0)
REVERT: A  262 ARG cc_start: 0.7336 (tmt-80) cc_final: 0.7117 (tpt90)
REVERT: A  266 LEU cc_start: 0.8012 (tp) cc_final: 0.7564 (tp)
REVERT: A  386 PHE cc_start: 0.7884 (m-80) cc_final: 0.7608 (m-80)
REVERT: A  502 GLU cc_start: 0.7071 (mp0) cc_final: 0.6867 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.1782
  time to fit residues: 31.6636
Evaluate side-chains
  127 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    3.9990
   chunk 65 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 43 optimal weight:    0.1980
   chunk 34 optimal weight:    0.8980
   chunk 67 optimal weight:    0.7980
   chunk 26 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 78 optimal weight:    0.8980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 198 GLN
A 396 GLN
A 608 GLN
A 902 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.197145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.176026 restraints weight = 11036.708|
|-----------------------------------------------------------------------------|
r_work (start): 0.4303 rms_B_bonded: 3.64
r_work: 0.4169 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.4169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6489
moved from start:          0.1598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7249  Z= 0.222
  Angle     :  0.614   7.142   9862  Z= 0.319
  Chirality :  0.045   0.168   1011
  Planarity :  0.005   0.040   1273
  Dihedral  :  4.878  22.706    946
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 13.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  9.69 %
    Favored  : 89.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.28), residues: 854
  helix:  0.07 (0.28), residues: 333
  sheet: -0.35 (0.57), residues: 87
  loop : -1.77 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 279 
 HIS   0.011   0.001   HIS A 275 
 PHE   0.015   0.001   PHE A 861 
 TYR   0.018   0.001   TYR A 531 
 ARG   0.004   0.000   ARG A 671 

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 142
  time to evaluate  : 0.707 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 HIS cc_start: 0.8030 (m-70) cc_final: 0.7819 (m170)
REVERT: A  234 TRP cc_start: 0.6038 (m100) cc_final: 0.4363 (m100)
REVERT: A  262 ARG cc_start: 0.7521 (tmt-80) cc_final: 0.7002 (tpt90)
REVERT: A  360 ILE cc_start: 0.7697 (tt) cc_final: 0.7349 (tt)
REVERT: A  386 PHE cc_start: 0.7898 (m-80) cc_final: 0.7532 (m-80)
REVERT: A  435 LYS cc_start: 0.7797 (tttt) cc_final: 0.7509 (tttm)
REVERT: A  439 MET cc_start: 0.7267 (mmp) cc_final: 0.6759 (mmp)
REVERT: A  502 GLU cc_start: 0.7513 (mp0) cc_final: 0.7072 (mp0)
REVERT: A  744 LYS cc_start: 0.8574 (tptp) cc_final: 0.8314 (tptp)
REVERT: A  803 PHE cc_start: 0.6638 (p90) cc_final: 0.5881 (p90)
  outliers start: 7
  outliers final: 4
  residues processed: 145
  average time/residue: 0.1985
  time to fit residues: 38.4139
Evaluate side-chains
  141 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 137
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  518 THR
Chi-restraints excluded: chain A residue  886 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 80 optimal weight:    0.0980
   chunk 35 optimal weight:    0.8980
   chunk 63 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 79 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 46 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   chunk 42 optimal weight:    0.1980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 198 GLN
A 283 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.196633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.175413 restraints weight = 11089.595|
|-----------------------------------------------------------------------------|
r_work (start): 0.4293 rms_B_bonded: 3.67
r_work: 0.4160 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.4160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6492
moved from start:          0.2093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7249  Z= 0.189
  Angle     :  0.559   7.644   9862  Z= 0.291
  Chirality :  0.043   0.166   1011
  Planarity :  0.004   0.043   1273
  Dihedral  :  4.802  22.474    946
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 12.96 %
    Favored  : 84.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.11 (0.28), residues: 854
  helix:  0.39 (0.29), residues: 332
  sheet: -0.33 (0.58), residues: 87
  loop : -1.76 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 850 
 HIS   0.015   0.001   HIS A 275 
 PHE   0.022   0.001   PHE A 861 
 TYR   0.018   0.001   TYR A 531 
 ARG   0.004   0.000   ARG A 887 

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 0.688 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 HIS cc_start: 0.7965 (m-70) cc_final: 0.7736 (m170)
REVERT: A  262 ARG cc_start: 0.7457 (tmt-80) cc_final: 0.7065 (tmt-80)
REVERT: A  415 ASN cc_start: 0.8508 (t0) cc_final: 0.8294 (t0)
REVERT: A  436 LYS cc_start: 0.7851 (ttpt) cc_final: 0.7644 (tptp)
REVERT: A  502 GLU cc_start: 0.7543 (mp0) cc_final: 0.7136 (mp0)
REVERT: A  744 LYS cc_start: 0.8504 (tptp) cc_final: 0.8281 (tptm)
REVERT: A  803 PHE cc_start: 0.6695 (p90) cc_final: 0.6041 (p90)
REVERT: A  815 ASP cc_start: 0.6159 (t0) cc_final: 0.5943 (t0)
REVERT: A  946 LYS cc_start: 0.7533 (mmmm) cc_final: 0.7321 (ttmm)
  outliers start: 18
  outliers final: 14
  residues processed: 140
  average time/residue: 0.1895
  time to fit residues: 35.6051
Evaluate side-chains
  144 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 130
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  283 ASN
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  371 PHE
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain A residue  518 THR
Chi-restraints excluded: chain A residue  588 MET
Chi-restraints excluded: chain A residue  747 GLU
Chi-restraints excluded: chain A residue  836 ILE
Chi-restraints excluded: chain A residue  886 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 28 optimal weight:    0.2980
   chunk 41 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 80 optimal weight:    0.7980
   chunk 56 optimal weight:    0.2980
   chunk 31 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 45 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 388 GLN
A 902 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4515 r_free = 0.4515 target = 0.198257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.176759 restraints weight = 11126.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.4284 rms_B_bonded: 3.71
r_work: 0.4150 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.4150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6510
moved from start:          0.2324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7249  Z= 0.193
  Angle     :  0.565   7.020   9862  Z= 0.292
  Chirality :  0.043   0.158   1011
  Planarity :  0.004   0.062   1273
  Dihedral  :  4.780  22.294    946
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 14.32 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.03 (0.29), residues: 854
  helix:  0.57 (0.29), residues: 332
  sheet: -0.40 (0.58), residues: 87
  loop : -1.79 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 850 
 HIS   0.010   0.001   HIS A 275 
 PHE   0.022   0.001   PHE A 861 
 TYR   0.016   0.001   TYR A 531 
 ARG   0.003   0.000   ARG A 887 

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 131
  time to evaluate  : 0.802 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 ARG cc_start: 0.7577 (tpp-160) cc_final: 0.7313 (tpp-160)
REVERT: A   81 GLN cc_start: 0.7356 (mp10) cc_final: 0.7079 (mp10)
REVERT: A   95 HIS cc_start: 0.7982 (m-70) cc_final: 0.7762 (m170)
REVERT: A  262 ARG cc_start: 0.7473 (tmt-80) cc_final: 0.7038 (tmt-80)
REVERT: A  390 GLU cc_start: 0.7503 (mp0) cc_final: 0.7260 (mp0)
REVERT: A  397 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7632 (tt)
REVERT: A  431 MET cc_start: 0.7570 (OUTLIER) cc_final: 0.7314 (ttm)
REVERT: A  502 GLU cc_start: 0.7563 (mp0) cc_final: 0.7094 (mp0)
REVERT: A  744 LYS cc_start: 0.8501 (tptp) cc_final: 0.8297 (tptm)
REVERT: A  803 PHE cc_start: 0.6745 (p90) cc_final: 0.6082 (p90)
REVERT: A  900 LYS cc_start: 0.8091 (mtpp) cc_final: 0.7865 (mtpp)
REVERT: A  946 LYS cc_start: 0.7549 (mmmm) cc_final: 0.7334 (ttmm)
  outliers start: 23
  outliers final: 13
  residues processed: 141
  average time/residue: 0.1991
  time to fit residues: 37.7150
Evaluate side-chains
  145 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 130
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  371 PHE
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  431 MET
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  518 THR
Chi-restraints excluded: chain A residue  588 MET
Chi-restraints excluded: chain A residue  747 GLU
Chi-restraints excluded: chain A residue  836 ILE
Chi-restraints excluded: chain A residue  886 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   chunk 45 optimal weight:    0.2980
   chunk 16 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 4 optimal weight:    0.0040
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.6396

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 902 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.197818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.176415 restraints weight = 10982.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.4287 rms_B_bonded: 3.68
r_work: 0.4150 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.4150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6517
moved from start:          0.2561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7249  Z= 0.193
  Angle     :  0.567   6.867   9862  Z= 0.295
  Chirality :  0.043   0.159   1011
  Planarity :  0.004   0.047   1273
  Dihedral  :  4.773  22.034    946
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 15.42 %
    Favored  : 82.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.01 (0.29), residues: 854
  helix:  0.66 (0.30), residues: 324
  sheet: -1.03 (0.54), residues: 99
  loop : -1.66 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 850 
 HIS   0.013   0.001   HIS A 275 
 PHE   0.016   0.001   PHE A 861 
 TYR   0.016   0.001   TYR A 531 
 ARG   0.003   0.000   ARG A 887 

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 0.693 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 ARG cc_start: 0.7592 (tpp-160) cc_final: 0.7337 (tpp-160)
REVERT: A   52 GLU cc_start: 0.6899 (mt-10) cc_final: 0.5825 (pt0)
REVERT: A   81 GLN cc_start: 0.7354 (mp10) cc_final: 0.7075 (mp10)
REVERT: A   95 HIS cc_start: 0.8021 (m-70) cc_final: 0.7811 (m170)
REVERT: A  234 TRP cc_start: 0.6173 (m100) cc_final: 0.4145 (m100)
REVERT: A  262 ARG cc_start: 0.7473 (tmt-80) cc_final: 0.7036 (tmt-80)
REVERT: A  366 PHE cc_start: 0.7366 (p90) cc_final: 0.7142 (p90)
REVERT: A  397 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7594 (tt)
REVERT: A  404 GLU cc_start: 0.7974 (tp30) cc_final: 0.7509 (tp30)
REVERT: A  436 LYS cc_start: 0.8047 (tptp) cc_final: 0.7732 (tptp)
REVERT: A  622 MET cc_start: 0.6618 (ppp) cc_final: 0.6385 (ppp)
REVERT: A  803 PHE cc_start: 0.6721 (p90) cc_final: 0.6073 (p90)
REVERT: A  900 LYS cc_start: 0.8103 (mtpp) cc_final: 0.7852 (mtpp)
REVERT: A  946 LYS cc_start: 0.7563 (mmmm) cc_final: 0.7344 (ttmm)
  outliers start: 18
  outliers final: 14
  residues processed: 140
  average time/residue: 0.2037
  time to fit residues: 38.1443
Evaluate side-chains
  146 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 131
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  371 PHE
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  431 MET
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  518 THR
Chi-restraints excluded: chain A residue  588 MET
Chi-restraints excluded: chain A residue  747 GLU
Chi-restraints excluded: chain A residue  866 LEU
Chi-restraints excluded: chain A residue  886 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 83 optimal weight:    0.7980
   chunk 27 optimal weight:    0.3980
   chunk 40 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 42 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 902 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.197387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4279 r_free = 0.4279 target = 0.175834 restraints weight = 10983.783|
|-----------------------------------------------------------------------------|
r_work (start): 0.4276 rms_B_bonded: 3.69
r_work: 0.4138 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.4138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6537
moved from start:          0.2706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7249  Z= 0.206
  Angle     :  0.577   6.927   9862  Z= 0.298
  Chirality :  0.043   0.168   1011
  Planarity :  0.004   0.049   1273
  Dihedral  :  4.791  22.052    946
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.03 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 16.23 %
    Favored  : 80.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.04 (0.29), residues: 854
  helix:  0.65 (0.30), residues: 327
  sheet: -0.90 (0.56), residues: 92
  loop : -1.74 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 850 
 HIS   0.010   0.001   HIS A 275 
 PHE   0.015   0.001   PHE A 861 
 TYR   0.017   0.002   TYR A 531 
 ARG   0.003   0.000   ARG A 387 

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 132
  time to evaluate  : 0.788 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 ARG cc_start: 0.7612 (tpp-160) cc_final: 0.7345 (tpp-160)
REVERT: A   52 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6077 (pt0)
REVERT: A   81 GLN cc_start: 0.7306 (mp10) cc_final: 0.7016 (mp10)
REVERT: A  234 TRP cc_start: 0.6200 (m100) cc_final: 0.4083 (m100)
REVERT: A  262 ARG cc_start: 0.7492 (tmt-80) cc_final: 0.6956 (tpt170)
REVERT: A  397 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7614 (tt)
REVERT: A  404 GLU cc_start: 0.7929 (tp30) cc_final: 0.7456 (tp30)
REVERT: A  436 LYS cc_start: 0.8028 (tptp) cc_final: 0.7684 (tptp)
REVERT: A  502 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.6752 (mp0)
REVERT: A  622 MET cc_start: 0.6620 (ppp) cc_final: 0.6368 (ppp)
REVERT: A  803 PHE cc_start: 0.6720 (p90) cc_final: 0.6032 (p90)
REVERT: A  900 LYS cc_start: 0.8070 (mtpp) cc_final: 0.7827 (mtpp)
REVERT: A  941 MET cc_start: 0.5088 (tpp) cc_final: 0.4693 (tpt)
REVERT: A  946 LYS cc_start: 0.7579 (mmmm) cc_final: 0.7355 (ttmm)
  outliers start: 25
  outliers final: 15
  residues processed: 142
  average time/residue: 0.1875
  time to fit residues: 35.9840
Evaluate side-chains
  146 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 129
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  371 PHE
Chi-restraints excluded: chain A residue  384 MET
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  431 MET
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  502 GLU
Chi-restraints excluded: chain A residue  518 THR
Chi-restraints excluded: chain A residue  747 GLU
Chi-restraints excluded: chain A residue  848 VAL
Chi-restraints excluded: chain A residue  866 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 37 optimal weight:    0.5980
   chunk 41 optimal weight:    0.1980
   chunk 66 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 30 optimal weight:    0.3980
   chunk 43 optimal weight:    0.3980
   chunk 80 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9980
   chunk 11 optimal weight:    0.2980
   overall best weight:    0.3780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 902 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4514 r_free = 0.4514 target = 0.198076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.176728 restraints weight = 11048.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.4293 rms_B_bonded: 3.68
r_work: 0.4158 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.4158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6481
moved from start:          0.2807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7249  Z= 0.161
  Angle     :  0.548   6.667   9862  Z= 0.283
  Chirality :  0.042   0.160   1011
  Planarity :  0.004   0.050   1273
  Dihedral  :  4.652  21.900    946
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 17.19 %
    Favored  : 80.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.05 (0.29), residues: 854
  helix:  0.68 (0.30), residues: 332
  sheet: -1.01 (0.56), residues: 94
  loop : -1.78 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 850 
 HIS   0.010   0.001   HIS A 275 
 PHE   0.015   0.001   PHE A 861 
 TYR   0.016   0.001   TYR A 531 
 ARG   0.002   0.000   ARG A 887 

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 136
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 ARG cc_start: 0.7576 (tpp-160) cc_final: 0.7328 (tpp-160)
REVERT: A   52 GLU cc_start: 0.6913 (mt-10) cc_final: 0.5767 (pt0)
REVERT: A  230 GLN cc_start: 0.6943 (tm-30) cc_final: 0.6576 (pt0)
REVERT: A  234 TRP cc_start: 0.6121 (m100) cc_final: 0.4116 (m100)
REVERT: A  262 ARG cc_start: 0.7506 (tmt-80) cc_final: 0.7076 (tmt-80)
REVERT: A  366 PHE cc_start: 0.7293 (p90) cc_final: 0.7081 (p90)
REVERT: A  397 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7545 (tt)
REVERT: A  404 GLU cc_start: 0.7923 (tp30) cc_final: 0.7463 (tp30)
REVERT: A  436 LYS cc_start: 0.8014 (tptp) cc_final: 0.7680 (tptp)
REVERT: A  502 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6795 (mp0)
REVERT: A  622 MET cc_start: 0.6624 (ppp) cc_final: 0.6384 (ppp)
REVERT: A  803 PHE cc_start: 0.6731 (p90) cc_final: 0.6125 (p90)
REVERT: A  900 LYS cc_start: 0.7999 (mtpp) cc_final: 0.7755 (mtpp)
REVERT: A  941 MET cc_start: 0.5136 (tpp) cc_final: 0.4755 (tpt)
REVERT: A  946 LYS cc_start: 0.7564 (mmmm) cc_final: 0.7344 (ttmm)
  outliers start: 20
  outliers final: 14
  residues processed: 146
  average time/residue: 0.1895
  time to fit residues: 37.3944
Evaluate side-chains
  148 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  431 MET
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  502 GLU
Chi-restraints excluded: chain A residue  518 THR
Chi-restraints excluded: chain A residue  662 THR
Chi-restraints excluded: chain A residue  747 GLU
Chi-restraints excluded: chain A residue  866 LEU
Chi-restraints excluded: chain A residue  886 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 66 optimal weight:    0.9980
   chunk 54 optimal weight:    0.2980
   chunk 35 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   chunk 43 optimal weight:    3.9990
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 902 HIS
** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4502 r_free = 0.4502 target = 0.196864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.175292 restraints weight = 11054.985|
|-----------------------------------------------------------------------------|
r_work (start): 0.4275 rms_B_bonded: 3.73
r_work: 0.4132 rms_B_bonded: 4.53 restraints_weight: 0.5000
r_work (final): 0.4132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6550
moved from start:          0.2915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7249  Z= 0.213
  Angle     :  0.597  10.174   9862  Z= 0.305
  Chirality :  0.044   0.160   1011
  Planarity :  0.004   0.053   1273
  Dihedral  :  4.831  21.743    946
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 17.60 %
    Favored  : 79.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.06 (0.29), residues: 854
  helix:  0.68 (0.30), residues: 332
  sheet: -0.89 (0.56), residues: 92
  loop : -1.83 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A 850 
 HIS   0.015   0.001   HIS A  95 
 PHE   0.017   0.001   PHE A 861 
 TYR   0.019   0.002   TYR A 531 
 ARG   0.004   0.000   ARG A 134 

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 129
  time to evaluate  : 0.715 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 ARG cc_start: 0.7612 (tpp-160) cc_final: 0.7339 (tpp-160)
REVERT: A   52 GLU cc_start: 0.6947 (mt-10) cc_final: 0.5971 (pt0)
REVERT: A  230 GLN cc_start: 0.7106 (tm-30) cc_final: 0.6766 (pt0)
REVERT: A  234 TRP cc_start: 0.6189 (m100) cc_final: 0.4165 (m100)
REVERT: A  262 ARG cc_start: 0.7526 (tmt-80) cc_final: 0.7007 (tmt-80)
REVERT: A  397 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7612 (tt)
REVERT: A  404 GLU cc_start: 0.7905 (tp30) cc_final: 0.7474 (tp30)
REVERT: A  436 LYS cc_start: 0.8011 (tptp) cc_final: 0.7659 (tptp)
REVERT: A  502 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.6753 (mp0)
REVERT: A  774 MET cc_start: 0.0969 (ptp) cc_final: 0.0739 (ptp)
REVERT: A  803 PHE cc_start: 0.6687 (p90) cc_final: 0.6000 (p90)
REVERT: A  900 LYS cc_start: 0.8108 (mtpp) cc_final: 0.7851 (mtpp)
REVERT: A  925 PHE cc_start: 0.6669 (OUTLIER) cc_final: 0.6372 (m-80)
REVERT: A  946 LYS cc_start: 0.7599 (mmmm) cc_final: 0.7380 (ttmm)
  outliers start: 19
  outliers final: 15
  residues processed: 139
  average time/residue: 0.1942
  time to fit residues: 36.2265
Evaluate side-chains
  147 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 129
  time to evaluate  : 0.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  371 PHE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  431 MET
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  502 GLU
Chi-restraints excluded: chain A residue  518 THR
Chi-restraints excluded: chain A residue  662 THR
Chi-restraints excluded: chain A residue  747 GLU
Chi-restraints excluded: chain A residue  866 LEU
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  925 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 28 optimal weight:    0.7980
   chunk 39 optimal weight:    0.0980
   chunk 22 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0870
   chunk 62 optimal weight:    3.9990
   overall best weight:    0.5358

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 902 HIS
** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.198577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.176931 restraints weight = 11132.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.4288 rms_B_bonded: 3.73
r_work: 0.4150 rms_B_bonded: 4.53 restraints_weight: 0.5000
r_work (final): 0.4150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6515
moved from start:          0.3014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7249  Z= 0.185
  Angle     :  0.592  12.084   9862  Z= 0.302
  Chirality :  0.043   0.162   1011
  Planarity :  0.004   0.054   1273
  Dihedral  :  4.794  21.838    946
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 12.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 18.28 %
    Favored  : 79.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.29), residues: 854
  helix:  0.65 (0.30), residues: 333
  sheet: -1.05 (0.55), residues: 94
  loop : -1.78 (0.29), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 850 
 HIS   0.007   0.001   HIS A 275 
 PHE   0.017   0.001   PHE A 861 
 TYR   0.018   0.001   TYR A 531 
 ARG   0.003   0.000   ARG A 134 

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 0.741 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 ARG cc_start: 0.7646 (tpp-160) cc_final: 0.7383 (tpp-160)
REVERT: A   52 GLU cc_start: 0.6980 (mt-10) cc_final: 0.5977 (pt0)
REVERT: A  230 GLN cc_start: 0.7066 (tm-30) cc_final: 0.6866 (pt0)
REVERT: A  234 TRP cc_start: 0.6146 (m100) cc_final: 0.4161 (m100)
REVERT: A  262 ARG cc_start: 0.7515 (tmt-80) cc_final: 0.7023 (tmt-80)
REVERT: A  397 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7596 (tt)
REVERT: A  404 GLU cc_start: 0.7919 (tp30) cc_final: 0.7492 (tp30)
REVERT: A  436 LYS cc_start: 0.7982 (tptp) cc_final: 0.7657 (tptp)
REVERT: A  502 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7198 (mt-10)
REVERT: A  803 PHE cc_start: 0.6717 (p90) cc_final: 0.6026 (p90)
REVERT: A  900 LYS cc_start: 0.8045 (mtpp) cc_final: 0.7796 (mtpp)
REVERT: A  925 PHE cc_start: 0.6664 (OUTLIER) cc_final: 0.6335 (m-80)
REVERT: A  941 MET cc_start: 0.5004 (tpp) cc_final: 0.4738 (tpt)
REVERT: A  946 LYS cc_start: 0.7575 (mmmm) cc_final: 0.7348 (ttmm)
  outliers start: 18
  outliers final: 13
  residues processed: 143
  average time/residue: 0.1923
  time to fit residues: 37.0878
Evaluate side-chains
  147 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  371 PHE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  431 MET
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  502 GLU
Chi-restraints excluded: chain A residue  518 THR
Chi-restraints excluded: chain A residue  662 THR
Chi-restraints excluded: chain A residue  866 LEU
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  925 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 73 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 37 optimal weight:    0.5980
   chunk 76 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    3.9990
   chunk 79 optimal weight:    0.5980
   chunk 30 optimal weight:    3.9990
   chunk 83 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.197097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.175509 restraints weight = 11273.057|
|-----------------------------------------------------------------------------|
r_work (start): 0.4270 rms_B_bonded: 3.77
r_work: 0.4132 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.4132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6548
moved from start:          0.3104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7249  Z= 0.215
  Angle     :  0.610  11.111   9862  Z= 0.313
  Chirality :  0.044   0.157   1011
  Planarity :  0.004   0.057   1273
  Dihedral  :  4.903  21.769    946
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 18.42 %
    Favored  : 78.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.29), residues: 854
  helix:  0.62 (0.30), residues: 333
  sheet: -0.68 (0.54), residues: 98
  loop : -1.91 (0.29), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 850 
 HIS   0.008   0.001   HIS A 275 
 PHE   0.018   0.001   PHE A 861 
 TYR   0.020   0.002   TYR A 531 
 ARG   0.003   0.000   ARG A 134 

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 131
  time to evaluate  : 0.764 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 ARG cc_start: 0.7711 (tpp-160) cc_final: 0.7441 (tpp-160)
REVERT: A   52 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6080 (pt0)
REVERT: A  234 TRP cc_start: 0.6199 (m100) cc_final: 0.4198 (m100)
REVERT: A  262 ARG cc_start: 0.7587 (tmt-80) cc_final: 0.6993 (tmt-80)
REVERT: A  397 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7638 (tt)
REVERT: A  404 GLU cc_start: 0.7900 (tp30) cc_final: 0.7471 (tp30)
REVERT: A  436 LYS cc_start: 0.7953 (tptp) cc_final: 0.7608 (tptp)
REVERT: A  450 VAL cc_start: 0.8146 (OUTLIER) cc_final: 0.7502 (t)
REVERT: A  502 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.6746 (mp0)
REVERT: A  755 PHE cc_start: 0.3424 (m-80) cc_final: 0.3203 (m-80)
REVERT: A  803 PHE cc_start: 0.6741 (p90) cc_final: 0.6019 (p90)
REVERT: A  900 LYS cc_start: 0.8073 (mtpp) cc_final: 0.7807 (mtpp)
REVERT: A  925 PHE cc_start: 0.6667 (OUTLIER) cc_final: 0.6364 (m-80)
REVERT: A  946 LYS cc_start: 0.7617 (mmmm) cc_final: 0.7394 (ttmm)
  outliers start: 19
  outliers final: 12
  residues processed: 141
  average time/residue: 0.2042
  time to fit residues: 39.0199
Evaluate side-chains
  147 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  371 PHE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  431 MET
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  502 GLU
Chi-restraints excluded: chain A residue  518 THR
Chi-restraints excluded: chain A residue  662 THR
Chi-restraints excluded: chain A residue  866 LEU
Chi-restraints excluded: chain A residue  925 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 72 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   overall best weight:    1.1784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  95 HIS
** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 902 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4474 r_free = 0.4474 target = 0.194452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.173013 restraints weight = 11012.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.4230 rms_B_bonded: 3.66
r_work: 0.4093 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.4093
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6606
moved from start:          0.3279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7249  Z= 0.292
  Angle     :  0.660  11.430   9862  Z= 0.340
  Chirality :  0.046   0.166   1011
  Planarity :  0.004   0.053   1273
  Dihedral  :  5.228  22.198    946
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 15.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.08 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 18.55 %
    Favored  : 78.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.29), residues: 854
  helix:  0.43 (0.29), residues: 335
  sheet: -0.99 (0.57), residues: 90
  loop : -1.94 (0.29), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A 850 
 HIS   0.007   0.001   HIS A 943 
 PHE   0.019   0.002   PHE A 861 
 TYR   0.023   0.002   TYR A 531 
 ARG   0.003   0.000   ARG A 134 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3518.96 seconds
wall clock time: 61 minutes 11.66 seconds (3671.66 seconds total)